# HG changeset patch
# User dfornika
# Date 1548180021 18000
# Node ID b102aece6b65f23e2de1fcb434463f1191f12ed9
# Parent  c92d935dc8abb6f367fe48e3f228f849e3eaadb6
planemo upload for repository https://github.com/tseemann/snippy commit 93b22331ca83a82fdfbe8f2b274577e21f9bf025-dirty

diff -r c92d935dc8ab -r b102aece6b65 snippy.xml
--- a/snippy.xml	Mon Jan 21 19:58:51 2019 -0500
+++ b/snippy.xml	Tue Jan 22 13:00:21 2019 -0500
@@ -40,23 +40,23 @@
                 --R2 '$fastq_input.fastq_input2'
             #end if
             #if str( $fastq_input.fastq_input_selector ) == "paired_collection"
-                --R1 '$fastq_input.fastq_input1.forward'
-                --R2 '$fastq_input.fastq_input1.reverse'
+                --R1 '$fastq_input.fastq_input.forward'
+                --R2 '$fastq_input.fastq_input.reverse'
             #end if
             #if str( $fastq_input.fastq_input_selector ) == "single"
-                --se '$fastq_input.fastq_input1'
+                --se '$fastq_input.fastq_input'
             #end if
             #if str( $fastq_input.fastq_input_selector ) == "paired_iv"
-                --peil '$fastq_input.fastq_input1'
+                --peil '$fastq_input.fastq_input'
             #end if
 
         &&
 
         #import re
-	#if str( $fastq_input.fastq_input_selector ) == "paired_collection"
-	    #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.forward.name)
+	#if str( $fastq_input.fastq_input_selector ) == "paired"
+	    #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
 	#else
-            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
+            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.element_identifier)
 	#end if
         mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ &&
 
@@ -81,13 +81,13 @@
                 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
             </when>
             <when value="single">
-                <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
+                <param name="fastq_input" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
             </when>
             <when value="paired_collection">
-                <param name="fastq_input1" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
+                <param name="fastq_input" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
             </when>
             <when value="paired_iv">
-                <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
+                <param name="fastq_input" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
             </when>
         </conditional>